Re: Can someone explain to me how both SD cards work at the same
Some apps aren't designed to work with storage the way the SGS3 does.
If you root, you can use a file exploring app to see that in /mnt (where storage gets "mounted"), there is a "sdcard" folder, and a "extSdCard" folder. Ext for "external." Samsung is treating the external SD card, or the MicroSD card you put in, as something different. Most all apps are hard-coded to save to /mnt/sdcard, which is the SGS3's "internal" storage.
It's a strange method, to say the least, and outside of waiting for apps to update and support Samsung's storage method, or a root app to create symlinks on the internal storage and moving the files to the microsd card specifically for the SGS3, it's unlikely you'll get a fix any time soon.